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(-) Description

Title :  CRYSTAL STRUCTURE OF RV2837C COMPLEXED WITH 5'-PAPA AND 5'-AMP
 
Authors :  F. Wang, Q. He, S. Liu, L. Gu
Date :  25 Apr 16  (Deposition) - 04 May 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Exonuclease, Dhh-Dhha1, C-Di-Amp Hydrolase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. He, F. Wang, S. Liu, D. Zhu, H. Cong, F. Gao, B. Li, H. Wang, Z. Lin, J. Liao, L. Gu
Structural And Biochemical Insight Into The Mechanism Of Rv2837C From Mycobacterium Tuberculosis As A C-Di-Nmp Phosphodiesterase
J. Biol. Chem. V. 291 14386 2016
PubMed-ID: 27371563  |  Reference-DOI: 10.1074/JBC.A115.699801
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN RV2837C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25177 / H37RA)
    Organism Taxid: 419947
    Strain: ATCC 25177 / H37RA
 
Molecule 2 - RNA (5'-R(P*AP*A)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:47 , ASP A:106 , HIS A:131 , ASP A:181 , HOH A:1129 , A C:1004binding site for residue MN A 1001
2AC2SOFTWAREHIS A:41 , ASP A:45 , ASP A:106 , HOH A:1129 , A C:1004binding site for residue MN A 1002
3AC3SOFTWAREASP B:47 , ASP B:106 , HIS B:131 , ASP B:181 , AMP B:1004binding site for residue MN B 1001
4AC4SOFTWAREHIS B:41 , ASP B:45 , ASP B:106 , AMP B:1004binding site for residue MN B 1002
5AC5SOFTWAREARG B:112 , HIS B:132 , GLU B:263 , SER B:292 , ARG B:294 , GLY B:309 , GLY B:310 , GLY B:311 , ALA B:315 , ALA B:316 , GLY B:317 , AMP B:1004 , HOH B:1125binding site for residue AMP B 1003
6AC6SOFTWAREASP B:45 , ASP B:106 , HIS B:131 , HIS B:132 , THR B:180 , ASP B:181 , TRP B:187 , ARG B:294 , HIS B:312 , ALA B:315 , MN B:1001 , MN B:1002 , AMP B:1003binding site for residue AMP B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JJU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:72 -Pro A:73
2Ala B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JJU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JJU)

(-) Exons   (0, 0)

(no "Exon" information available for 5JJU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh.hhhhh.hhhhh.....eeeee...hhhhhhhhhhhh.....eeeee..........eeee.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhh.eee.hhhhhh.eeeeeehhhhhhhhhhhhh.hhhhhhh......eeeeeeeee..eeeeeeee....hhhhhhh...eee..eeeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jju A   18 GARVDAVGAAALLSAAARVGVVCHVHPDADTIGAGLALALVLDGCGKRVEVSFAAPATLPESLRSLPGCHLLVRPEVMRRDVDLVVTVDIPSVDRLGALGDLTDSGRELLVIDHHASNDLFGTANFIDPSADSTTTMVAEILDAWGKPIDPRVAHCIYAGLATDTGSFRWASVRGYRLAARLVEIGVDNATVSRTLMDSHPFTWLPLLSRVLGSAQLVSEAVGGRGLVYVVVDNREWVAARSEEVESIVDIVRTTQQAEVAAVFKEVEPHRWSVSMRAKTVNLAAVASGFGGGGHRLAAGYTTTGSIDDAVASLRAALGLTRAPP  342
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     


Chain B from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh.hhhhh...........eeeee...hhhhhhhhhhhhhh...eeeee..........eeee.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhh..eee.hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh......eeeeeeeee..eeeeeeee....hhhhhhhh..ee...eeeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jju B   18 GARVDAVGAAALLSAAARVGVVCHVHPDADTIGAGLALALVLDGCGKRVEVSFAAPATLPESLRSLPGCHLLVRPEVMRRDVDLVVTVDIPSVDRLGALGDLTDSGRELLVIDHHASNDLFGTANFIDPSADSTTTMVAEILDAWGKPIDPRVAHCIYAGLATDTGSFRWASVRGYRLAARLVEIGVDNATVSRTLMDSHPFTWLPLLSRVLGSAQLVSEAVGGRGLVYVVVDNREWVAARSEEVESIVDIVRTTQQAEVAAVFKEVEPHRWSVSMRAKTVNLAAVASGFGGGGHRLAAGYTTTGSIDDAVASLRAALGLTRAPP  342
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     


Chain C from PDB  Type:RNA  Length:2
                                   
                5jju C 1003 AA 1004
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JJU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JJU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JJU)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:72 - Pro A:73   [ RasMol ]  
    Ala B:72 - Pro B:73   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

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